People knowledgeable about the term told The Wall Street Journal that this phrase was a "rallying cry." Basically, if it looked like the company, region, or dealer wasn't going to hit sales targets, this was a sign that some outside-the-box sales solutions were needed. People told the news outlet those solutions could include selling cars at a loss or having the dealer buy a fleet of customer test-drive cars.
However, this could also be evidence of some less savory ways to boost sales. In addition to the investigation, the company is already facing at least one lawsuit from a dealer group that alleges it would bribe dealers to pad monthly sales figures. FCA had an incentive to maintain sales numbers as well, considering that it was claiming a long streak of increasing sales.
Under scrutiny recently, the company changed its sales reporting practices and numbers for previous years. Under the old reporting methods, it was possible for dealers to sell cars, report the sales, and then cancel or "unwind" the sales later. This wouldn't count as a lost sale, but the car also couldn't be recorded as another sale later. As a result, an unscrupulous dealer could have hypothetically used it to "sell" a car one month and "unwind" it the next. If FCA knew about this, it's also possible the company could have pushed dealers to use the system for false sales, something the Feds theorize may be related to the "unnatural acts department" phrase.
It's still entirely possible this "unnatural acts department" was just a corporate term for thinking of creative ways to meet sales goals. And selling cars at a loss is definitely unnatural for businesses that are trying to make money. Whatever the phrase truly meant to dealers, it certainly is bizarre.